BIOL 263: Molecular Biology and Genomics
Fall Semester 2006
Last modified Nov 28, 2006
We are currently on schedule.
(Latest update overrides all previous versions, electronic and print.)
MWF 10:10 AM-11:00 AM (Period 3)
Tomsich Hall Room 101
(Owen York Lecture Hall)
Dr. Wade Powell
FSH 202, PBX 5396
powellw[a]kenyon.edu
Office hours: M 11 AM - noon and 1-2 PM; TR, 8:45-9:45 AM; F, 11AM - noon
(or by appointment)
Introduction:
The molecular and genomic basis of life is at the heart of modern biology. In BIOL 263, we will learn techniques and explore research questions at the forefront of molecular research, focusing on the mechanisms by which the information of the genome is expressed to form the functional molecules of living cells and organisms. The processes of DNA replication, recombination and repair, transcription of RNA from DNA templates, and translation of RNA into protein are discussed in the context of current research, frequently using primary literature. The function of genes and regulation and measurement of gene expression are treated in depth. Students analyze and publish interactive tutorials on the structure and function of key macromolecules. This intermediate-level course presumes a strong background in the basics of protein structure/function, central dogma processes, fundamental molecular techniques for manipulating nucleic acids and proteins, and general chemistry.
Required prerequisites: BIOL 113, 114; one year of chemistry (Intro or Honors Intro); or permission of the instructor.
Recommended prerequisite or co-requisite: CHEM 231 and 232 (Organic Chemistry).
Reading Materials and Resources:
- Required text: Watson et al., (2004) Molecular Biology of the Gene, 5th edition.
- Journal Articles are linked to syllabus and/or provided in class.
- Web resources will be used in class and for your assignments.
- Pokescope for stereo viewing is purchased through the Biology department.
All reading assignments must be completed before class on the date indicated on syllabus.
Policies and Expectations:
- Class attendance: 100% attendance is expected, and absences will detract from one's grade. Please see me immediately about conflicts due to sports events, performances, religious holidays, etc.
- Class participation: To participate fully in class, you must thoughtfully read the assigned material before each meeting. Expect to be called on; raise your hand! Please feel free to ask questions, add insights, correct the instructor's innacuracies, etc. at any time during class.
- Scheduling and Deadlines. Please plan carefully. Exam schedules and deadlines for submitting assigned work are firm, and extensions will not be granted for conflcits with the workload for other courses. Accomodations due to illness or other personal situation must be requested through the Dean of Students or the Health and Counseling Center.
- Academic Honesty. Do not lie, cheat, or plagiarize. Do your own work on exams. In writing projects, properly acknowledge your sources of information, and acknowledge the help you receive from others. Kenyon's policy on academic honesty (pp. 26-29 of the Course of Study) will be strictly observed. Explicit guidelines relating to final projects or other collaborative assignments will be discussed in class.
- Special Needs. For assistance related to a physical, psychological or learning disability that may impact your ability to participate fully in the course, please speak with me and with Erin Salva, Coordinator of Disability Services (PBX5453; salvae@kenyon.edu). All information and documentation of disability is confidential. Please see the Disability Services web site for more information.
Assignments and Grades: Your grade is based on performance in the following areas:
- 10% Attendance and Participation. 100% attendance is expected, including one Thursday seminar. To participate fully in class, you must thoughtfully read and annotate the assigned material before each meeting. Active, vocal participation is expected from all members of the class and will be the primary determinant of class participation grade.
- 10% Quizzes. Eight to ten quizzes over the semester. Quizzes will be unannounced. NOTE: Make-up quizzes will not be possible. Please don't ask. To compensate for conflicts due to athletics, performances, illnesses, busy schedules, etc., you may skip up to two quizzes without penalty or prior permission.
- 60% Three Exams (each 20%). There are three regular exams in class.
- 20% Molecular Tutorial Project. A JMol Molecular Tutorial Project substitutes for the final exam. It is recommended that two partners share a project. Examples of past projects and instructions for creating new onew can be viewed at Biomolecules at Kenyon. A working model must be ready for presentation to the class on Dec. 8 . The final version, with zero broken links, is due December 18 at 11:30am (time corresponds to the scheduled time for the final exam). Both partners share full responsibility for the completed project.
Important Links:
(Note: Some resources can only be accessed on Kenyon campus.)
- Web resources
- Biomolecules at Kenyon
- Find Molecules: PDB and NIH
- Watson text
- Stereo molecules
Course Schedule
| Day | Date | Topic | Reading | Notes | Work Due |
Part I: Molecular Interactions |
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| M | Aug 28 | Course Introduction. DNA intro; 3D; B-DNA; A-RNA; DNA & RNA |
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| W | Aug 30 | Weak bonds. Amino Acids; CAP; FAB; Ident | Watson Ch 3; Ch 5, pp. 69-73 | Notes | |
| F | Sept 1 | Adv DNA. FT; Z-DNA ; HIV; Triplex; Quad; base tautomers; supercoiling; Topo | Watson Ch 6 | Notes | |
| M | Sept 4 | AA2 in proteins. | Ch 5 p 73-92; | Notes | |
| W | Sept 6 | Introduction to crystallography methods; basic X-Ray; |
Protein Purification: Ch. 20, pp. 672-675. basic X-ray; "Molecules of Life;" more advanced X-Ray (local version); another explanation (pdf). |
Notes | |
| F | Sept 8 | DNA-protein binding; Vocab; Human ADAR1; ADAR activity and consequence |
Schwartz 99; Reading journal articles. |
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Part II: Gene Expression |
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| M | Sept 11 | Transcription initiation Structures: RnaPol-Bact; RnaPol-Euk |
Watson Ch 12 pp. 347-363; | Notes | |
| W | Sept 13 | Transcription Elongation; transcriptional road blocks Structures: RnaPol-Bact; RnaPol-Euk |
Epshtein & Nudler 2003 [Background: Conaway et al. 2003 (2nd and 3rd paragraphs)] |
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| F | Sept 15 | Bacterial Gene Regulation at level of transcription initiation. CAP-CTD ; Benoff |
Watson Ch 16, pp. 483-504 | Notes | |
| M | Sept 18 | Regulation of intiation, cont'd; Regulation of events after initiation: Attenuation in E. coli. |
Watson Ch 16, pp.504-511; |
Notes | |
| W | Sept 20 | Attenuation in Bacillus. TRAP-RNA; |
Antson 99; Watson Ch. 16, pp. 509-510; |
Notes | |
| F | Sept 22 | Transcriptional regulation without regulatory proteins: Riboswitches. Breaker Lab Riboswitch site (Yale) &movie |
Soukup 2004 review |
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| M | Sept 25 | Exam I (in class) Points to ponder for the exam. | |||
| W | Sept 27 | Eukaryotic Basal Transcription Factors. DAB PolII; TBP; TAF |
Watson Ch. 12 pp.363-377; Ch. 16, Box 16-1 (pp. 490-491); Ch. 20, pp. 672-675. |
Notes | |
| F | Sept 29 | Eukaryotic Transcriptional Regulation; Spec. TFs. Activators; Identify |
Watson Ch, 17, pp. 529-555; | Notes | |
| M | Oct 2 | Eukaryotic Transcription, cont'd. | . | . | |
| W | Oct 4 | Eukaryotic Transcription Research: Promoter Clearance | Pal et al. 2005 | ||
| R | Oct 5 4:00 PM |
Biology Dept. Seminar: Dr. Donal Luse, Lerner Research Institute, Cleveland Clinic Foundation "Mechanism of promoter clearance by RNA polymerase II" |
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| F | Oct 6 | Nucleosomes & Transcriptional regulation; Histone Code. Figures; Nucleosome | Watson Ch. 7 pp. 151-180; Ch. 17 p. 540 & pp. 556-562. Histone binding sites: Nature N&V 2006 |
Notes | |
| M | Oct 9 | October Reading Days; No Class | |||
| W | Oct 11 | Research in Eukaryotic Transcriptional Regulation: Histone acetyltransferase recruitment | Sharma 2002 Chromatin IP; cross-link chemistry Remember PCR? |
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| F | Oct 13 | Transcript Splicing; Lupus; Splicing2; Spliceosome | Watson Ch. 13 | Notes | JMol Project: PDB Proposal |
| M | Oct 16 | Translation initiation. Initiation. PDB | Watson Ch. 14, pp. 411-439. | Notes | |
| W | Oct 18 | Translation elongation, termination. | Watson Ch. 14. pp. 440-459. | Notes | |
| F | Oct 20 | Finish translation process; "Protein Jive Sutra" |
Watson Ch. 14. | ||
| M | Oct 23 | Translation in the Nucleus? Notes Nonsense-mediated decay |
Iborra 01 | ||
| W | Oct 25 | RNA Interference Animation from Nature Reviews Genetics . |
Meister
04 (RNAi review paper) Watson Ch. 17 pp. 567-570 |
Notes | |
| F | Oct 27 | Argonaute in RNAi | Liu 04 * supporting materials |
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| M | Oct 30 | Exam II (points to ponder) | |||
Part III: DNA Replication, Repair, Recombination |
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| W | Nov 1 | DNA Replication; Beta ring; DNA Rep; Replisome | Watson Ch. 8 | Notes | |
| F | Nov 3 | DNA Rep., cont'd.; | Watson Ch. 8 |
Notes | |
| M | Nov 6 | Mutation and repair. | Watson Ch. 9 | Notes | Web Project Workshop, FSH 009, 7-10 PM |
| T | Nov 7 | Web Project Workshop, FSH 009, 7-10 PM | |||
| W | Nov 8 | MutS; MutS-DNA; Figs. | Obmolova 00 | Class activity: Student descriptions for mock tutorial | |
| R | Nov 9 | Web Project Workshop, FSH 009, 7-10 PM | |||
| F | Nov 10 | Recombination; Experiments; RuvA; PNAS; Tn; | Watson Ch. 10 | Notes | |
| M | Nov 13 | Telomerase and telomeres | Watson Ch. 8 p. 229-232. Blackburn 2000 review |
Notes | Telomeres 12-mer; 22-mer |
| W | Nov 15 | Telomerase depletion and cancer cell division | Li et al. 2005 | ||
| F | Nov 17 | Knockout mice in molecular biology | |||
| Nov 18-26 | Thanksgiving Break | ||||
Part IV: Genomic-scale molecular biology |
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| M | Nov 27 | Genomes: Human Genome; Ensembl Black heart drug; Designer Babies |
Watson Ch. 2, p. 38-39; Ch. 7, p. 133-138; Ch. 20, p. 660-671. | Notes | |
| W | Nov 29 | Schulze 2001 review article Watson Ch. 18, pp. 575-577 |
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| F | Dec 1 | Microarray Research: Diurnal & circadian related gene expression | Schaffer et al. 2001 Supplemental material |
Guided meditation | |
| M | Dec 4 | Catch up and review | . | . | . |
| W | Dec 6 | Exam III (points to ponder) | . | . | . |
| F | Dec 8 | Student Project Presentations | . |
. | Completed JMol Tutorial |
| M | Dec 11 | Student Project Presentations | . | . | . |
| M | Dec 18 | Revised JMol Tutorials Due | No Broken Links | 11:30 AM | |
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